arXiv subjects

Yohei Nakayama

Publications and source records attributed to Yohei Nakayama.

13 recordsLinked to original sources

arXiv2025

Acceleration of enzymatic reaction-diffusion kinetics by intermediate state

Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the initial and final primary states. However, the influence of these intermediate states on motor performance has not yet been fully explored. In this study, we investigate the impact of intermediate states on the motor kinetics using a reaction-diffusion model. In most cases, the intermediate states accelerate the motor by lowering the effective barrier height. This acceleration is particularly pronounced when an external load is applied to the motor, implying the practical importance of the intermediate states. The intermediate states can also slow down the reaction in some cases, such as the slow reaction limit with asymmetric kinetics. Our findings provide practical insights into the design principles behind the high performance of biological molecular motors, as well as the development of efficient artificial molecular motors.

physics.bio-ph↗

arXiv2025

Asymmetric enzyme kinetics of F1-ATPase induced by rotation-assisted substrate binding

We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1-ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis, which is an F1-ATPase's primary biological role, deviates from it. Specifically, the synthesis rate is sustained even at low substrate concentrations. Analysis of a theoretical model consistent with the experimental results reveals that ATP synthesis implements a rotation-assisted mechanism, in which a limited binding rate at low substrate concentration is partially compensated for by rotation to an angle where the binding rate is high. The results may imply that F1-ATPase implements a regulatory mechanism of enhancing substrate binding for ATP synthesis.

physics.bio-ph↗

arXiv2025

Efficiently driving F$_1$ molecular motor in experiment by suppressing nonequilibrium variation

F$_1$-ATPase (F$_1$) is central to cellular energy transduction. Forcibly rotated by another motor F$_\mathrm{o}$, F$_1$ catalyzes ATP synthesis by converting mechanical work into chemical free energy stored in the molecule ATP. The details of how F$_\mathrm{o}$ drives F$_1$ are not fully understood; however, evaluating efficient ways to rotate F$_1$ could provide fruitful insights into this driving since there is a selective pressure to improve efficiency. Here, we show that rotating F$_1$ with an angle clamp is significantly more efficient than a constant torque. Our experiments, combined with theory and simulation, indicate that the angle clamp significantly suppresses the nonequilibrium variation that contributes to the futile dissipation of input work.

physics.bio-ph↗

arXiv2025

Experimentally achieving minimal dissipation via thermodynamically optimal transport

Optimal transport theory, originally developed in the 18th century for civil engineering, has since become a powerful optimization framework across disciplines, from generative AI to cell biology. In physics, it has recently been shown to set fundamental bounds on thermodynamic dissipation in finite-time processes. This extends beyond the conventional second law, which guarantees zero dissipation only in the quasi-static limit and cannot characterize the inevitable dissipation in finite-time processes. Here, we experimentally realize thermodynamically optimal transport using optically trapped microparticles, achieving minimal dissipation within a finite time. As an application to information processing, we implement the optimal finite-time protocol for information erasure, confirming that the excess dissipation beyond the Landauer bound is exactly determined by the Wasserstein distance - a fundamental geometric quantity in optimal transport theory. Furthermore, our experiment achieves the bound governing the trade-off between speed, dissipation, and accuracy in information erasure. To enable precise control of microparticles, we develop scanning optical tweezers capable of generating arbitrary potential profiles. Our work establishes an experimental approach for optimizing stochastic thermodynamic processes. Since minimizing dissipation directly reduces energy consumption, these results provide guiding principles for designing high-speed, low-energy information processing.

cond-mat.stat-mech↗

arXiv2024

SatSwinMAE: Efficient Autoencoding for Multiscale Time-series Satellite Imagery

Recent advancements in foundation models have significantly impacted various fields, including natural language processing, computer vision, and multi-modal tasks. One area that stands to benefit greatly is Earth observation, where these models can efficiently process large-scale, unlabeled geospatial data. In this work we extend the SwinMAE model to integrate temporal information for satellite time-series data. The architecture employs a hierarchical 3D Masked Autoencoder (MAE) with Video Swin Transformer blocks to effectively capture multi-scale spatio-temporal dependencies in satellite imagery. To enhance transfer learning, we incorporate both encoder and decoder pretrained weights, along with skip connections to preserve scale-specific information. This forms an architecture similar to SwinUNet with an additional temporal component. Our approach shows significant performance improvements over existing state-of-the-art foundation models for all the evaluated downstream tasks: land cover segmentation, building density prediction, flood mapping, wildfire scar mapping and multi-temporal crop segmentation. Particularly, in the land cover segmentation task of the PhilEO Bench dataset, it outperforms other geospatial foundation models with a 10.4% higher accuracy.

cs.CV↗

arXiv2021

Optimal rectification without forward-current suppression by biological molecular motor

We experimentally showed that biological molecular motor F$_1$-ATPase (F$_1$) implements an optimal rectification mechanism. F$_1$ hardly suppresses adenosine triphosphate (ATP) synthesis, which is the F$_1$'s physiological role while inhibiting unfavorable hydrolysis of ATP. This optimal rectification is a high contrast to a simple ratchet model, where the inhibition of the backward current is inevitably accompanied by the suppression of the forward current. The detailed analysis of single-molecule trajectories demonstrated a novel but simple rectification mechanism of F$_1$ with parallel landscapes and asymmetric transition rates.

physics.bio-ph↗

arXiv2020

Effective Langevin equations leading to large deviation function of time-averaged velocity for a nonequilibrium Rayleigh piston

We study fluctuating dynamics of a freely movable piston that separates an infinite cylinder into two regions filled with ideal gas particles at the same pressure but different temperatures. To investigate statistical properties of the time-averaged velocity of the piston in the long-time limit, we perturbatively calculate the large deviation function of the time-averaged velocity. Then, we derive an infinite number of effective Langevin equations yielding the same large deviation function as in the original model. Finally, we provide two possibilities for uniquely determining the form of the effective model.

cond-mat.stat-mech↗

arXiv2020

Stochastic order parameter dynamics for phase coexistence in heat conduction

We propose a stochastic order parameter equation for describing phase coexistence in steady heat conduction near equilibrium. By analyzing the stochastic dynamics with a non-equilibrium adiabatic boundary condition, where total energy is conserved over time, we derive a variational principle that determines thermodynamic properties in non-equilibrium steady states. The resulting variational principle indicates that the temperature of the interface between the ordered region and the disordered region becomes greater (less) than the equilibrium transition temperature in the linear response regime when the thermal conductivity in the ordered region is less (greater) than that in the disordered region. This means that a super-heated ordered (super-cooled disordered) state appears near the interface, which was predicted by an extended framework of thermodynamics proposed in [N. Nakagawa and S.-i. Sasa, Liquid-gas transitions in steady heat conduction, Phys. Rev. Lett. {\bf 119}, 260602, (2017).]

cond-mat.stat-mech↗

arXiv2019

Multiplicative Langevin Equation to Reproduce Long-time Properties of Nonequilibrium Brownian Motion

We statistically examine long time sequences of Brownian motion for a nonequilibrium version of the Rayleigh piston model and confirm that the third cumulant of a long-time displacement for the nonequilibrium Brownian motion linearly increases with the observation time interval. We identify a multiplicative Langevin equation that can reproduce the cumulants of the long-time displacement up to at least the third order, as well as its mean, variance and skewness. The identified Langevin equation involves a velocity-dependent friction coefficient that breaks the time-reversibility and may act as a generator of the directionality. Our method to find the Langevin equation is not specific to the Rayleigh piston model but may be applied to a general time sequence in various fields.

cond-mat.stat-mech↗

arXiv2018

The Entropy Anomaly and the Linear Irreversible Thermodynamics

The irreversible currents and entropy production rate of a dilute colloidal suspension are calculated using the linear irreversible thermodynamics and the linear response theory. The \anomalous" or \hidden" entropy recently discussed in the context of the stochastic thermodynamics is fully accounted in these classic frameworks. We show that the two distinct formulations lead to identical results as long as the local equilibrium assumption or, equivalently the linear response theory, is valid.

cond-mat.stat-mech↗

arXiv2018

Unattainability of Carnot efficiency in thermal motors: Coarse-graining and entropy production of Feynman-Smoluchowski ratchet

We revisit and analyze the thermodynamic efficiency of the Feynman-Smoluchowski (FS) ratchet, a classical thought experiment describing an autonomous heat-work converter. Starting from the full kinetics of the FS ratchet and deriving the exact forms of the hidden dissipations resulting from coarse-graining, we restate the historical controversy over its thermodynamic efficiency. The existence of hidden entropy productions implies that the standard framework of stochastic thermodynamics applied to the coarse-grained descriptions fails in capturing the dissipative feature of the system. In response to this problem, we explore an extended framework of stochastic thermodynamics to reconstruct the hidden entropy production from the coarse-grained dynamics. The approach serves as a key example of how we can systematically address the problem of thermodynamic efficiency in a multi-variable fluctuating non-equilibrium system.

cond-mat.stat-mech↗

arXiv2015

Invariance of Steady State Thermodynamics between Different Scales of Description

By considering general Markov stochastic dynamics and its coarse-graining, we study the framework of stochastic thermodynamics for the original and reduced descriptions corresponding to different scales. We are especially concerned with the case where the irreversible entropy production has a finite difference between the scales. We find that the sum of increment of nonequilibrium entropy and excess part of entropy production, which are key quantities in construction of steady state thermodynamics, is essentially kept invariant with respect to the change in the scales of description. This general result justifies experimental approaches toward steady state thermodynamics based on coarse-grained variables. We demonstrate our result in a mesoscopic heat engine system.

cond-mat.stat-mech↗

arXiv2012

Fluctuation Theorem for Hidden Entropy Production

In the general process of eliminating dynamic variables in Markovian models, there exists a difference in the irreversible entropy production between the original and reduced dynamics. We call this difference the hidden entropy production, since it is an invisible quantity when only the reduced system's view is provided. We show that this hidden entropy production obeys a new integral fluctuation theorem for the generic case where all variables are time-reversal invariant, therefore supporting the intuition that entropy production should decrease by coarse graining. It is found, however, that in cases where the condition for our theorem does not hold, entropy production may also increase due to the reduction. The extended multibaker map is investigated as an example for this case.

cond-mat.stat-mech↗